Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects.

BACKGROUND: Smoking remains one of the leading preventable causes of death. Smoking leaves a strong signature on the blood methylome as shown in multiple studies using the Infinium HumanMethylation450 BeadChip. Here, we explore novel blood methylation smoking signals on the Illumina MethylationEPIC BeadChip (EPIC) array, which also targets novel CpG-sites in enhancers. METHOD: A smoking-methylation meta-analysis was carried out using EPIC DNA methylation profiles in 1407 blood samples from four UK population-based cohorts, including the MRC National Survey for Health and Development (NSHD) or 1946 British birth cohort, the National Child Development Study (NCDS) or 1958 birth cohort, the 1970 British Cohort Study (BCS70), and the TwinsUK cohort (TwinsUK). The overall discovery sample included 269 current, 497 former, and 643 never smokers. Replication was pursued in 3425 trans-ethnic samples, including 2325 American Indian individuals participating in the Strong Heart Study (SHS) in 1989-1991 and 1100 African-American participants in the Genetic Epidemiology Network of Arteriopathy Study (GENOA). RESULTS: Altogether 952 CpG-sites in 500 genes were differentially methylated between smokers and never smokers after Bonferroni correction. There were 526 novel smoking-associated CpG-sites only profiled by the EPIC array, of which 486 (92%) replicated in a meta-analysis of the American Indian and African-American samples. Novel CpG sites mapped both to genes containing previously identified smoking-methylation signals and to 80 novel genes not previously linked to smoking, with the strongest novel signal in SLAMF7. Comparison of former versus never smokers identified that 37 of these sites were persistently differentially methylated after cessation, where 16 represented novel signals only profiled by the EPIC array. We observed a depletion of smoking-associated signals in CpG islands and an enrichment in enhancer regions, consistent with previous results. CONCLUSION: This study identified novel smoking-associated signals as possible biomarkers of exposure to smoking and may help improve our understanding of smoking-related disease risk.

Saccharomyces cerevisiae Rbg1 protein and its binding partner Gir2 interact on Polyribosomes with Gcn1.

Rbg1 is a previously uncharacterized protein of Saccharomyces cerevisiae belonging to the Obg/CgtA subfamily of GTP-binding proteins whose members are involved in ribosome function in both prokaryotes and eukaryotes. We show here that Rbg1 specifically associates with translating ribosomes. In addition, in this study proteins were identified that interact with Rbg1 by yeast two-hybrid screening and include Tma46, Ygr250c, Yap1, and Gir2. Gir2 contains a GI (Gcn2 and Impact) domain similar to that of Gcn2, an essential factor of the general amino acid control pathway required for overcoming amino acid shortage. Interestingly, we found that Gir2, like Gcn2, interacts with Gcn1 through its GI domain, and overexpression of Gir2, under conditions mimicking amino acid starvation, resulted in inhibition of growth that could be reversed by Gcn2 co-overexpression. Moreover, we found that Gir2 also cofractionated with polyribosomes, and this fractionation pattern was partially dependent on the presence of Gcn1. Based on these findings, we conclude that Rbg1 and its interacting partner Gir2 associate with ribosomes, and their possible biological roles are discussed.

Polar location of the chemoreceptor complex in the Escherichia coli cell.

The eukaryotic cell exhibits compartmentalization of functions to various membrane-bound organelles and to specific domains within each membrane. The spatial distribution of the membrane chemoreceptors and associated cytoplasmic chemotaxis proteins in Escherichia coli were examined as a prototypic functional aggregate in bacterial cells. Bacterial chemotaxis involves a phospho-relay system brought about by ligand association with a membrane receptor, culminating in a switch in the direction of flagellar rotation. The transduction of the chemotaxis signal is initiated by a chemoreceptor-CheW-CheA ternary complex at the inner membrane. These ternary complexes aggregate predominantly at the cell poles. Polar localization of the cytoplasmic CheA and CheW proteins is dependent on membrane-bound chemoreceptor. Chemoreceptors are not confined to the cell poles in strains lacking both CheA and CheW. The chemoreceptor-CheW binary complex is polarly localized in the absence of CheA, whereas the chemoreceptor-CheA binary complex is not confined to the cell poles in strains lacking CheW. The subcellular localization of the chemotaxis proteins may reflect a general mechanism by which the bacterial cell sequesters different regions of the cell for specialized functions.

Requirement of the carboxyl terminus of a bacterial chemoreceptor for its targeted proteolysis.

The bacterium Caulobacter crescentus yields two different progeny at each cell division; a chemotactically competent swarmer cell and a sessile stalked cell. The chemotaxis proteins are synthesized in the predivisional cell and then partition only to the swarmer cell upon division. The chemoreceptors that were newly synthesized were located at the nascent swarmer pole of the predivisional cell, an indication that asymmetry was established prior to cell division. When the swarmer cell differentiated into a stalked cell, the chemoreceptor was specifically degraded by virtue of an amino acid sequence located at its carboxyl terminus. Thus, a temporally and spatially restricted proteolytic event was a component of this differentiation process.

Increasing Access to Physical Activity Within Low Income and Diverse Communities: A Systematic Review.

OBJECTIVE: The purpose of this review is to uncover some best practices for increasing access to physical activity opportunities by examining efforts used within low income and diverse communities. The theoretical lens used is from the Active Living by Design (ALbD) Community Action Model, with a focus on the 6 essential practices (health equity focus, community engagement, facilitative leadership, sustainable thinking, culture of learning, and strategic communication) describing how partnerships can guide and sustain meaningful change in a community. METHODS: A 2-step process guided the literature search. In step 1, 4 databases (PubMed, Psych INFO, Social Science Citation Index, and Cochrane Library) were searched using Boolean connections and variations in the key terms. Step 2 assessed articles by title, abstract, and full text to determine whether the studies met the inclusion and exclusion criteria guided by Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Additionally, included articles were compared against the 6 essential practices outlined by the ecological framework, ALbD. RESULTS: Of 1775 total articles, 14 studies met inclusion criteria. Most of the studies were case studies located in the United States using several different approaches including, changes in the built environment, implementation of a community-based physical activity program, creating partnerships to leverage resources, and policy change. This review compared the 14 studies against the 6 essential practices of the ALbD model and found 2 studies that met all 6 criteria, and only a few studies meeting more than 2 criteria. CONCLUSIONS: Overall, the conclusions are 2-fold, (1) only 14 cases demonstrate success in increasing access to physical activity opportunities, suggesting that more can be done to address inequalities. (2) Of the existing efforts, few utilize crucial components to create a sustainable change in the community. Future research should take into consideration the ALbD ecological framework, the best existing theory for this type of work, to guide the creation and implementation of a sustainable community access effort.

Childhood adversity and DNA methylation in two population-based cohorts.

Childhood adversity affects later health, but the underlying molecular mechanisms are unclear. Although there is some evidence from animal models and case-control studies of a role for DNA methylation, evidence from human population-based studies is limited. In two cohorts (mothers from the Avon Longitudinal Study of Parents and Children, ALSPAC, n = 780 and women from the MRC National Survey of Health and Development, NSHD, n = 552), we assessed the association of seven adverse childhood experiences (ACEs: parental physical illness, parental mental illness, parental death, parental separation, suboptimal maternal bonding, childhood illness and child maltreatment) as well as their combination (ACE score) with genome-wide DNA methylation levels measured using the Illumina Infinium HumanMethylation450 BeadChip in peripheral blood at mean age 47 years (ALSPAC) and in buccal cells at age 53 years (NSHD). CpG sites with a genome-wide false discovery rate (FDR) below 0.05 and differentially methylated regions (DMRs) with one-step Sidák correction p-values below 0.05 in each cohort were examined in the other cohort. No individual CpG sites replicated across cohorts. However, nine DMRs replicated across cohorts respectively associated with the ACE score (one region), parental mental illness (two regions), parental physical illness (three regions) and parental death (three regions). These observations indicate that some adverse childhood experiences, notably those related to parental health, may leave imprints on peripheral DNA methylation that persist to mid-life.

Bacterial sporulation: pole-to-pole protein oscillation.

Sporulating bacteria need to temporally coordinate DNA replication, chromosome partitioning and sporulation initiation. Recent work has shown that one aspect of this coordination lies with the interdependent subcellular localization of two proteins, Spo0J and Soj, and in the Spo0J-dependent spatial oscillation of Soj.

Bacterial division: Finding the dividing line.

Division of a cell - whether eukaryotic or prokaryotic - requires accurate spatial coordination. Recent work on the bacterium Escherichia coli has shown that correct placement of the cell division site at the midcell position occurs by a combination of selection against potential polar sites and selection of the midcell site.

Evidence for related functions of the RNA genes of Saccharomyces cerevisiae.

The yeast genes RNA2-RNA11 are necessary for splicing of nuclear intron-containing pre-mRNAs. We investigated the relationships among these genes by asking whether increased expression of one RNA gene leads to suppression of the temperature-sensitive lethality of a mutation in any other RNA gene. The presence of extra plasmid-borne copies of the RNA3 gene relieves the lethality of temperature-sensitive rna4 mutations. A region of the yeast genome (SRN2) is described that suppresses temperature-sensitive rna2 mutations when it is present on either medium or high-copy number plasmids. Neither suppression occurs via a bypass of RNA gene function since null alleles of rna2 and rna4 are not suppressed by elevated dosage of SRN2 and RNA3, respectively. These results suggest that the SRN2 and RNA2 gene products have related functions, as do the RNA3 and RNA4 gene products.

Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes.

The PRP4 gene encodes a protein that is a component of the U4/U6 small nuclear ribonucleoprotein particle and is necessary for both spliceosome assembly and pre-mRNA splicing. To identify genes whose products interact with the PRP4 gene or gene product, we isolated second-site suppressors of temperature-sensitive prp4 mutations. We limited ourselves to suppressors with a distinct phenotype, cold sensitivity, to facilitate analysis of mutants. Ten independent recessive suppressors were obtained that identified four complementation groups, spp41, spp42, spp43 and spp44 (suppressor of prp4, numbers 1-4). spp41-spp44 suppress the pre-mRNA splicing defect as well as the temperature-sensitive phenotype of prp4 strains. Each of these spp mutations also suppresses prp3; spp41 and spp42 suppress prp11 as well. Neither spp41 nor spp42 suppressors null alleles of prp3 or prp4, indicating that the suppression does not occur via a bypass mechanism. The spp41 and spp42 mutations are neither allele- nor gene-specific in their pattern of suppression and do not result in a defect in pre-mRNA splicing. Thus the SPP41 and SPP42 gene products are unlikely to participate directly in mRNA splicing or interact directly with Prp3p or Prp4p. Expression of PRP3-lacZ and PRP4-lacZ gene fusions is increased in spp41 strains, suggesting that wild-type Spp41p represses expression of PRP3 and PRP4. SPP41 was cloned and sequenced and found to be essential. spp43 is allelic to the previously identified suppressor srn1, which encodes a negative regulator of gene expression.

The Chlamydomonas zygospore: mutant strains of Chlamydomonas monoica blocked in zygospore morphogenesis comprise 46 complementation groups.

Chlamydomonas monoica undergoes homothallic sexual reproduction in response to nitrogen starvation. Mating pairs are established in clonal culture via flagellar agglutination and fuse by way of activated mating structures to form the quadriflagellate zygote. The zygote further matures into a dormant diploid zygospore through a series of events that we collectively refer to as zygosporulation. Mutants that arrest development prior to the completion of zygosporulation have been obtained through the use of a variety of mutagens, including ultraviolet irradiation, 5-fluorodeoxyuridine, ethyl methanesulfonate, and methyl methanesulfonate. Complementation analysis indicates that the present mutant collection includes alleles affecting 46 distinct zygote-specific functions. The frequency with which alleles at previously defined loci have been recovered in the most recent mutant searches suggests that as many as 30 additional zygote-specific loci may still remain to be identified. Nevertheless, the present collection should provide a powerful base for ultrastructural, biochemical, and molecular analysis of zygospore morphogenesis and dormancy in Chlamydomonas.

25-hydroxyvitamin D, APOE ɛ4 genotype and cognitive function: findings from the 1958 British birth cohort.

Both high and low vitamin D statuses have been associated with lower memory function. Apolipoprotein E (APOE) ɛ4 alleles have been associated with reduced memory function, and separately with higher vitamin D concentrations. This report aims to examine if the presence of APOE ɛ4 alleles contributes to the relationship between vitamin D and memory function. A total of 4848 (46% female) participants from the 1958 British birth cohort had information on APOE genotypes and completed memory tests at 50 years, where 4644 also had 25-hydroxyvitamin D (25(OH)D) concentrations measured at 45 years. Both low and high 25(OH)D concentrations were associated with lower memory function after adjustment for number of APOE ɛ4 alleles (P curvature=0.02). There was evidence of interaction between APOE ɛ4 and 25(OH)D, suggesting the association between 25(OH)D concentrations and memory function is different for those with two APOE ɛ4 alleles compared with those with zero or one APOE ɛ4 alleles (recessive model P interaction=0.01). Among participants with two APOE ɛ4 alleles, higher 25(OH)D concentrations were associated with higher memory function, whereas in others, memory scores were slightly lower for individuals with higher versus lower concentrations. Further studies are required to replicate these findings.

Plasma GABA-like activity in response to ethanol challenge in men at high risk for alcoholism.

Sons of alcoholic fathers (high risk, HR) and matched control men from families without alcoholism (low risk, LR) were administered, in a randomized double-blind fashion, either a placebo beverage or an isovolemic beverage containing ethanol (0.8 g/kg). Serial blood sampling for determination of plasma gamma-aminobutyric acid (GABA)-like activity, mood, and intoxication ratings were performed. The HR subjects were found to have significantly less plasma GABA-like activity than LR during the placebo condition. The alcoholic beverage condition washed out the differences in plasma GABA between groups. Significant interactions between risk group status and beverage conditions were found with respect to plasma GABA-like activity. Alcohol produced an increase in mean GABA-like activities among HR subjects, whereas a slight decline was noted among LR subjects. Plasma GABA-like activity also had a significant inverse correlation with self-reports of perceived tension in the placebo condition, and tension, confusion, and intoxication in response to the alcoholic drink. Since previous investigators have reported reduced plasma GABA levels in alcoholic individuals, reduced plasma GABA-like activity may be a biological marker for vulnerability to alcoholism or for heightened tension as a behavioral factor that predisposes to alcoholism.

The N-terminal domain of the Caulobacter crescentus CgtA protein does not function as a guanine nucleotide exchange factor.

The Caulobacter crescentus GTP binding protein CgtA is a member of the Obg/GTP1 subfamily of monomeric GTP binding proteins. In vitro, CgtA displays moderate affinity for both GDP and GTP, and rapid exchange rate constants for either nucleotide. One possible explanation for the observed rapid guanine nucleotide exchange rates is that CgtA is a bimodal protein with a C-terminal GTP binding domain and an N-terminal guanine nucleotide exchange factor (GEF) domain. In this study we demonstrate that although the N-terminus of CgtA is required for function in vivo, this domain plays no significant role in the guanine nucleotide binding, exchange or GTPase activity.

The N-terminal domain of the Caulobacter crescentus CgtA protein does not function as a guanine nucleotide exchange factor.

The Caulobacter crescentus GTP binding protein CgtA is a member of the Obg/GTP1 subfamily of monomeric GTP binding proteins. In vitro, CgtA displays moderate affinity for both GDP and GTP, and rapid exchange rate constants for either nucleotide. One possible explanation for the observed rapid guanine nucleotide exchange [corrected] rates is that CgtA is a bimodal protein with a C-terminal GTP binding domain and an N-terminal GEF domain. In this study we demonstrate that although the N-terminus of CgtA is required for function in vivo, this domain plays no significant role in the guanine nucleotide binding, exchange or GTPase activity.

Guidelines for assessment and treatment of sexual dysfunction.

This article presents a diagnostic and treatment planning guide that can be used when a patient complains of a sexual problem. The basic principles are summarized in the form of a grid. The axes of the grid represent "problem focus" and "influencing variables." The grid can be used to aid in diagnosis, to assess the severity of a sexual problem, to suggest a direction for treatment, and to guide referral.

Statistical power of articles published in three health psychology-related journals.

Power was calculated for 8,266 statistical tests in 187 journal articles published in the 1997 volumes of Health Psychology (HP), Addictive Behaviors (AB), and the Journal of Studies on Alcohol (JSA). Power to detect small, medium, and large effects was .34. .74. and .92 for HP; .34, .75, and .90 for AB; and .41, .81. and .92 for JSA. Mean power estimates are .36, .77, and .91, giving a good estimation for the field of health psychology. J. Cohen (1988) recommended that power to detect effects should be approximately .80. Using this criterion, the articles in these journals have adequate power to detect medium and large effects. Intervention studies have much less power to detect effects than nonintervention studies do. Results are encouraging for this field, although studies examining small effects are still very much underpowered. This issue is important, because most intervention effects in health psychology are small.

The influence of alclofenac treatment on acute-phase proteins, plasma tryptophan, and erythrocyte sedimentation rate in patients with rheumatoid arthritis.

Alclofenac and D-penicillamine were compared under controlled, double-blind conditions in the treatment of 35 patients with active rheumatoid arthritis over a period of 26 weeks. The principal aim of the study was to investigate any relationships between changes in clinical status and changes in concentrations of three serum acute-phase proteins (fibrinogen, C-reactive protein, and haptoglobin), plasma free and protein-bound L-tryptophan, and the erythrocyte sedimentation rate. Both alclofenac and D-penicillamine were clearly effective: all patients showed steady improvement on the seven clinical indices of response employed. Drug management was easiest with alclofenac. Both drugs produced a significant reduction in acute-phase proteins, E.S.R. and protein-bound plasma tryptophan. Since it has previously been established that the course of rheumatoid arthritis is reflected in the acute-phase protein levels and the extent to which L-tryptophan is bound to plasma protein, it is suggested that drugs, such as D-penicillamin and alclofenac which profoundly affect these parameters, provide not only symptomatic relief but also possible beneficial effects on the disease process itself.

Treatment of rheumatoid arthritis with tolmetin: a comparison with alclofenac.

A double-blind between-patient trial over 6 weeks to compare the effects of 1.6 g tolmetin daily with 4 g alclofenac daily was completed by 37 out of 44 out-patients with rheumatoid arthritis. Tolmetin proved as effective as alclofenac in relieving pain and in reducing both the articular index score and the number of inflamed joints. However, alclofenac produced a significantly greater reduction in the duration of morning stiffness, which could have been related to the timing of the initial daily dose of tolmetin. Onset of fatigue was significantly improved by both drugs. Neither treatment group exhibited any significant changes in the serum levels of IgG, IgA, and IgM, nor in the latex and sheep-cell agglutination titres. Although neither drug gave rise to serious side-effects, 3 patients (2 on tolmetin, 1 on alclofenac) were withdrawn because of skin rash, 2 (on tolmetin) because of gastro-intestinal upsets, and 1 from each group because of lack of analgesic effects.